plotSpikeRG              package:CALIB              R Documentation

_p_l_o_t _s_p_i_k_e _i_n_t_e_n_s_i_t_y _R _v_s _G

_D_e_s_c_r_i_p_t_i_o_n:

     plot red intensity vs green intensity of spikes.

_U_s_a_g_e:

     plotSpikeRG(spike,parameter,RG,array = 1, bc = FALSE, area = TRUE,
                 xlab = "log(Rintensity)", ylab = "log(Gintensity)",
                 main = colnames(spike$R)[array], onlycalib = FALSE, 
                 xlim = NULL, ylim = NULL, pch = 19, cex = 0.3, col = "black", 
                 allpch = 19, allcex = 0.05, allcol = "lightgrey", diag = TRUE,
                 diagcol = "grey", diaglwd = 1, curvecol = "blue",
                 curvelwd = 1.5, calibtype = 1, adjusttype = 4, ...)

_A_r_g_u_m_e_n_t_s:

   spike: a 'SpikeList' object.

parameter: a 'ParameterList object.'. If 'parameter' argument is
          sepcified, model curves are shown on the plot. 

      RG: a 'RGList_CALIB object'. If 'parameter' argument is
          specified, this argument is obligated. More description in
          Detail section.

   array: integer giving the array to be plotted. 

      bc: a logical value. 'TRUE' means background corrected measured 
          intensities are used. Default is 'FALSE'.

    area: a logical value. 'TRUE' means spot area is used to calculate 
          measured intensities. Namly, measured intensities are
          calculated by  foreground intensities(or background corrected
          intensities, if bc is  'TRUE') multiply spot area. 'FALSE'
          means spot area is not used. Default is 'TRUE'.

    xlab: a title for the x axis.

    ylab: a title for the y axis.

    main: an overall title for the plot.

onlycalib: a logical value. 'TRUE' means only the calibration controls
          are on  the plot. 'FALSE' means to plot all the spikes

    xlim: the x limits (min,max) of the plot.

    ylim: the y limits (min,max) of the plot.

     pch: an integer code for one of a set of plotting characters or
          symbols for the spike data set. Default is 21.

     cex: a numerical value giving the amount by which the points which
           indicate spike data set should be scaled relative to the
          default. Default is 0.3.

     col: the color of the points indicating spike data set. Default is
          black.

  allpch: an integer code for one of a set of plotting characters or
          symbols for the spike data set. Default is 19. 

  allcex: a numerical value giving the amount by which the points which
           indicate all data set should be scaled relative to the
          default. Default is 0.05. 

  allcol: the color of the points indicating all data set. Default is
          lightgrey.

    diag: a logical value. Add diagonal on the plot if it is 'TRUE'.
          Default is 'TRUE'.

 diagcol: the color of the diagonal. Default is grey.

 diaglwd: the width of the diagonal. Default is 1.

curvecol: the color of the model curves. Default is blue.

curvelwd: the width of the model curves for calibration control spikes.
          Default is 1.5.

calibtype: the line type of the model curves for  calibration control
          spikes. Default is 1.

adjusttype: the line type of the model curves (using parameter after
          adjustment) for calibration control spikes. Default is 4.

     ...: other graphical parameters can be used in function 'plot'. 

_D_e_t_a_i_l_s:

     The function plots red vs green measured intensities of spikes of
     one array.  The argument 'array' gives the array index to be
     plotted. 

     If parameter estimation is done, the model curves can be plotted
     by giving the argument 'parameter'. And if the argument
     'parameter' is specified, the argument 'RG' is obligated. The
     combination of these two arguments is used to compare how the
     model fits to the spike and to the whole data set. More details
     about the usage of this function refers to the readme file of this
     package.

     It supports different ways to calculate the measured intensities. 
     Arguments 'bc' and 'area' are logical and their combinations are
     used  for specifying four differents ways. 'bc' indicates using
     background correction or not. 'area' indicates multipling spot
     area or not. The default value of these two arguments are 'bc' =
     FALSE and 'area' = TRUE. 

     see other graphic functions for the other arguments.

_V_a_l_u_e:

     A plot is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Hui Zhao

_E_x_a_m_p_l_e_s:

     # load data: spike
     data(spike)

     # specify the array to be plotted.
     array <- 1

     # use the default values for other arguments
     plotSpikeRG(spike,array=array)

     # after parameter estimation, the model curves can be shown on the plot.
     data(parameter)
     data(RG)
     plotSpikeRG(spike,parameter,RG)

